@JDesat: The database gets corrupted because something went wrong. It could be a bug in the software, it could be that you didn't eject the device safely one time, it could have been a crash.
The only case I have been able to prove a reason for a corrupt database has been when reading CBZ or CBR files and then connecting to the PC. That was a bug on the device not freeing things properly. This was fixed recently in either the 4.28 or 4.30 firmware.
Looking at the errors, the only way that might fix it is the VACUUM, or compress, of the database. That basically dumps the database out and reloads it. It should clean up everything. But, there is a chance that some data will be lost. Most of those errors should be harmless and a sign that some cleanup wasn't done. The first two are
Rebuilding an index won't help. When that has been suggested, it was because the check showed that there was an index problem. And it named the index that needed to be rebuilt.
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